User:Steven Tuyishime

Undergraduate student at UMBC, Group consisits of Sindhu Lakkur, Ejiofor Ezekwe and Steven Tuyishime- Dr. Thomas Gluick Biol 430



Glutamine Synthetase CATH Domains
Glutamine Synthetase (GS) has 2 prominent CATH domains. CATH is an acronym for Class (C), Architecture (A), Topology (T), and Homologous superfamily (H), which are categories for protein classification. Each of the aforementioned levels are used to classify molecules in a hierarchical manner. The highest order classification of a molecule is Class. A molecule can be classified by any one of 4 classes: Mainly Alpha, Mainly Beta, Alpha Beta, and Few Secondary Structures. Another level of classification which is on a lower order than class is Architecture. This level of classification is used to identify the shape of the domain structure using the orientation of secondary structures but ignoring the way they are connected to each other. A third level of classification is Topology, which is also called Fold Group. This classification concerns the shared similarity of overall shape and connectivity of the secondary structures in the domain core. The Homologous superfamily refers to a fourth classification type. This hierarchy groups together protein domains which are thought to share a common ancestor, according to specific criteria.

Looking at Glutamine Synthetase in Salmonella typhimurium, we can identify 2 CATH domains, with the smaller domain encompassing residues 1-103 (in red) and the other residues 104-456 (in blue). Each of the domains are of the class Alpha Beta, however, that is the only common aspect between the two. Alpha Beta includes both alternating alpha/beta structures and alpha+beta structures. One domain begins at residue 104 and goes to residue 456. For this domain, the Architecture is a 2 layer sandwich, another example of a 2 layer sandwich can be found at http://www.cathdb.info/cathnode/3.30. A 2 layer sandwich consists of a layer of alpha helices and a layer of beta sheets forming a sandwich like structure. The Topology is Creatine Kinase; Chain A, domain 2 and the Homologous superfamily is Creatine Kinase; Chain. This domain is the larger of the two and has a COOH terminus.

The second domain in S. typhimurium begins at residue 1 and goes to residue 103. In this domain, the architecture is a roll because the alpha helices and beta sheets form a roll-like structure. The topology is ubiquitin-like, or a UB-roll due to its resemblance to a cartoon depiction of ubiquitin and the Homologous superfamily has no defined name. This domain is smaller and has an NH2 terminus. It is covalently linked to the larger COOH terminus(the first domain described in prior paragraph). This NH2 terminus is exposed compared to the buried COOH terminus of the larger domain.

For more information on CATH and the different classifications that are defined, consult the article by Orengo et al or visit the cath website at http://www.cathdb.info/